But I assume they did not write the game in Python and the optimize parts in C++. Quite the opposite - they wrote it in C++ and then found that some part (e.g. GUI) is growing in complexity while not being crucial for performance, at which point it is a good decision to use a scripting language for it.

That is a pretty common approach, but what was suggested above (writing first in HLL and then rewriting parts in C++) is, to my knowledge, never done in practice.